Unexpected loss of files and source code without a clear cause

[Toquetzin]

Type: Bug

I’ve been editing code with the help of the Copilot agent, and I worked for two days using its assistance. Once I finished, I saved the files and closed the editor. Now, at the start of the week, I opened the project to continue working and discovered that everything I worked on last week is gone — the code has been deleted, files are blank, and previously deleted files have reappeared empty.
What is going on here? This is not a functional tool; it’s harmful. Please provide an explanation. This appears to be a very serious issue. I didn’t do anything unusual: I simply opened the editor, edited code, requested help from Copilot Agent, saved my work, and closed the application.

Extension version: 0.29.1
VS Code version: Code 1.102.1 (7adae6a, 2025-07-15T16:41:17.147Z)
OS version: Windows_NT x64 10.0.22631
Modes:

Logs

Trace: choice {"delta":{"content":null,"tool_calls":[{"function":{"arguments":"K\\\" "},"index":0}]}}
Trace: choice {"delta":{"content":null,"tool_calls":[{"function":{"arguments":"// Especi"},"index":0}]}}
Trace: choice {"delta":{"content":null,"tool_calls":[{"function":{"arguments":"ficar "},"index":0}]}}
Trace: choice {"delta":{"content":null,"tool_calls":[{"function":{"arguments":"que es t"},"index":0}]}}
Trace: choice {"delta":{"content":null,"tool_calls":[{"function":{"arguments":"eléfono"},"index":0}]}}
Trace: choice {"delta":{"content":null,"tool_calls":[{"function":{"arguments":" de tr"},"index":0}]}}
Trace: choice {"delta":{"content":null,"tool_calls":[{"function":{"arguments":"abaj"},"index":0}]}}
Trace: choice {"delta":{"content":null,"tool_calls":[{"function":{"arguments":"o\\n    "},"index":0}]}}
Trace: choice {"delta":{"content":null,"tool_calls":[{"function":{"arguments":"   "},"index":0}]}}
Trace: choice {"delta":{"content":null,"tool_calls":[{"function":{"arguments":"    "},"index":0}]}}
Trace: choice {"delta":{"content":null,"tool_calls":[{"function":{"arguments":"     }\"}"},"index":0}]}}
Trace: choice {"finish_reason":"tool_calls","delta":{"content":null}}
Info: message 0 returned. finish reason: [tool_calls]
Debug: message 0 details: finishOffset: [undefined] completionId: [{msg_01VxCLFazJLbXynHUb8oVidw}] created: [{1753142770}]
Info: request done: requestId: [90e98db3-d7a3-4b29-97b7-4b81eb83e594] model deployment ID: []
Info: ccreq:a4189f58.copilotmd | success | claude-sonnet-4 | 3699ms | [panel/editAgent]
Trace: Resolving chat model
Trace: Resolved chat model
Trace: Resolving chat model
Trace: Resolved chat model
Debug: AgentIntent: rendering with budget=90639 (baseBudget: 112000, toolTokens: 5365), summarizationEnabled=true
Trace: Resolving chat model
Trace: Resolving chat model
Trace: Resolved chat model
Trace: Resolved chat model
Trace: [NES][Triggerer][onDidChangeTextDocument] created
Trace: [NES][Triggerer][onDidChangeTextDocument] Return: ignored document
Trace: [NES][Triggerer][onDidChangeTextDocument] created
Trace: [NES][Triggerer][onDidChangeTextDocument] Return: ignored document
Trace: [NES][Triggerer][onDidChangeTextDocument] created
Trace: [NES][Triggerer][onDidChangeTextDocument] Return: ignored document
Trace: [NES][Triggerer][onDidChangeTextDocument] created
Trace: [NES][Triggerer][onDidChangeTextDocument] Return: ignored document
Debug: Related Information: Index not loaded yet triggering background calculation, returning 0ms
Trace: Resolving chat model
Trace: Resolved chat model
Trace: Resolving chat model
Trace: Resolved chat model
Trace: Resolving chat model
Trace: Resolved chat model
Trace: Resolving chat model
Trace: Resolved chat model
Trace: Built prompt
Trace: Sending prompt to model
Debug: modelMaxPromptTokens 112000
Debug: modelMaxResponseTokens 16000
Debug: chat model claude-sonnet-4
Trace: g0.initialize#24 started
Trace: g0.initialize#24 success. Elapsed 0.052300000097602606
Debug: Embeddings for commandEmbeddings calculated in 2571ms

Request IDs

aa52bc61-52c0-4e0e-8761-03155e6f1ea0
8e393811-84de-4da7-b9f4-04bdff5e2daa
aed0d663-e509-4af6-aa3d-853ce11cba98
3ade87a3-dc4e-4fa8-9caa-7d307d0a463a
424092d9-1f95-47c9-be25-dc18013e203d
aad272a3-eb98-4a68-ace3-609b52c152f0
42bc29b1-42fd-4002-84eb-4e466c3e505b
90e98db3-d7a3-4b29-97b7-4b81eb83e594

System Info

Item	Value
CPUs	AMD Ryzen 9 5950X 16-Core Processor (16 x 3400)
GPU Status	2d_canvas: unavailable_software canvas_oop_rasterization: disabled_off direct_rendering_display_compositor: disabled_off_ok gpu_compositing: disabled_software multiple_raster_threads: enabled_on opengl: disabled_off rasterization: disabled_software raw_draw: disabled_off_ok skia_graphite: disabled_off video_decode: disabled_software video_encode: disabled_software vulkan: disabled_off webgl: unavailable_software webgl2: unavailable_software webgpu: unavailable_software webnn: unavailable_software
Load (avg)	undefined
Memory (System)	12.48GB (4.54GB free)
Process Argv	--crash-reporter-id 5118dad2-ed8d-4f50-b82c-85317d8d17af
Screen Reader	no
VM	0%

[hediet]

Related #256570?

[Toquetzin]

I believe there are more than two ways code can be lost — it had already happened to me before, but in a different way. During my first days using GitHub Copilot in agent mode, I downloaded a copy of a project developed in PHP. It needed some improvements, so I asked Copilot to help me review the CSS and make a few adjustments. It completed the task successfully and began analyzing the project’s code to determine where to apply updates for the new CSS classes.

After all the adjustments were made and tested correctly, I noticed that a few extensions (two or three, I’m not sure) were showing update notifications. I decided to apply the updates by clicking “Restart extensions,” and that alone was enough to cause the entire project to go blank in an instant. Every file that Copilot had reviewed was empty — even files where no changes were made. I tried undoing or restoring the changes, but everything remained blank.

I immediately suspected GitHub Copilot and realized how serious this issue is. No warning or notice is provided about this when purchasing the license or subscription — just a general message stating “Copilot may make mistakes; always review the code.”

Since the tool is actually useful to me, I continued using it, but with a series of precautions. I started creating fresh chats and deleting previous ones. I stopped installing extensions while Copilot is active. Usually, after Copilot finishes something, I close it, wait a few minutes, reopen it, and double-check that nothing was deleted. I verify the output and continue working.

But this last time, I followed the same steps — except I didn’t delete the chat. I simply closed Copilot and kept working. I left the editor and my computer running all weekend. When I resumed the project at the beginning of the week, I briefly closed the editor, restarted the computer… and to my surprise, the files were gone again.

[Toquetzin]

@hediet

Related #256570?

It’s similar, but he’s only reporting the issue of deleted files reappearing. In my case, I’m also seeing previously deleted files come back, but they’re completely blank — and the most critical part is that I’m losing actual code.